+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7tdt | ||||||||||||
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タイトル | Cryo-EM structure of nanodisc-embedded human ABCA1 | ||||||||||||
要素 | Phospholipid-transporting ATPase ABCA1 | ||||||||||||
キーワード | MEMBRANE PROTEIN / sterol transport / ABC transporter / phospholipid transport | ||||||||||||
機能・相同性 | 機能・相同性情報 sphingolipid floppase activity / regulation of high-density lipoprotein particle assembly / apolipoprotein A-I receptor activity / positive regulation of high-density lipoprotein particle assembly / Defective ABCA1 causes TGD / signal release / response to vitamin B3 / apolipoprotein A-I binding / platelet dense granule organization / intracellular cholesterol transport ...sphingolipid floppase activity / regulation of high-density lipoprotein particle assembly / apolipoprotein A-I receptor activity / positive regulation of high-density lipoprotein particle assembly / Defective ABCA1 causes TGD / signal release / response to vitamin B3 / apolipoprotein A-I binding / platelet dense granule organization / intracellular cholesterol transport / high-density lipoprotein particle binding / phospholipid transporter activity / HDL assembly / floppase activity / response to laminar fluid shear stress / phosphatidylserine floppase activity / protein transmembrane transport / peptide secretion / cellular response to cholesterol / phosphatidylcholine floppase activity / export across plasma membrane / phosphatidylcholine binding / phospholipid homeostasis / phospholipid efflux / cholesterol transfer activity / reverse cholesterol transport / high-density lipoprotein particle assembly / P-type phospholipid transporter / lipoprotein biosynthetic process / regulation of Cdc42 protein signal transduction / syntaxin binding / phospholipid translocation / cholesterol efflux / endosomal transport / cholesterol binding / phagocytosis, engulfment / intracellular vesicle / lysosome organization / negative regulation of cholesterol storage / cellular response to cytokine stimulus / apolipoprotein binding / endocytic vesicle / ATPase-coupled transmembrane transporter activity / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / protein transmembrane transporter activity / ABC-type transporter activity / protein secretion / positive regulation of cholesterol efflux / cellular response to retinoic acid / phagocytic vesicle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cholesterol metabolic process / cholesterol homeostasis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / PPARA activates gene expression / small GTPase binding / cellular response to xenobiotic stimulus / ATPase binding / cellular response to lipopolysaccharide / basolateral plasma membrane / endosome / G protein-coupled receptor signaling pathway / membrane raft / external side of plasma membrane / intracellular membrane-bounded organelle / signaling receptor binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / ATP binding / plasma membrane 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4 Å | ||||||||||||
データ登録者 | Plummer, A.M. / Culbertson, A.T. / Morales-Perez, C.L. / Liao, M. | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: J Mol Biol / 年: 2023 タイトル: Activity and Structural Dynamics of Human ABCA1 in a Lipid Membrane. 著者: Ashlee M Plummer-Medeiros / Alan T Culbertson / Claudio L Morales-Perez / Maofu Liao / 要旨: The human ATP-binding cassette (ABC) transporter ABCA1 plays a critical role in lipid homeostasis as it extracts sterols and phospholipids from the plasma membrane for excretion to the extracellular ...The human ATP-binding cassette (ABC) transporter ABCA1 plays a critical role in lipid homeostasis as it extracts sterols and phospholipids from the plasma membrane for excretion to the extracellular apolipoprotein A-I and subsequent formation of high-density lipoprotein (HDL) particles. Deleterious mutations of ABCA1 lead to sterol accumulation and are associated with atherosclerosis, poor cardiovascular outcomes, cancer, and Alzheimer's disease. The mechanism by which ABCA1 drives lipid movement is poorly understood, and a unified platform to produce active ABCA1 protein for both functional and structural studies has been missing. In this work, we established a stable expression system for both a human cell-based sterol export assay and protein purification for in vitro biochemical and structural studies. ABCA1 produced in this system was active in sterol export and displayed enhanced ATPase activity after reconstitution into a lipid bilayer. Our single-particle cryo-EM study of ABCA1 in nanodiscs showed protein induced membrane curvature, revealed multiple distinct conformations, and generated a structure of nanodisc-embedded ABCA1 at 4.0-Å resolution representing a previously unknown conformation. Comparison of different ABCA1 structures and molecular dynamics simulations demonstrates both concerted domain movements and conformational variations within each domain. Taken together, our platform for producing and characterizing ABCA1 in a lipid membrane enabled us to gain important mechanistic and structural insights and paves the way for investigating modulators that target the functions of ABCA1. | ||||||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7tdt.cif.gz | 335.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7tdt.ent.gz | 265.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7tdt.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 7tdt_validation.pdf.gz | 835.3 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7tdt_full_validation.pdf.gz | 858.6 KB | 表示 | |
XML形式データ | 7tdt_validation.xml.gz | 56.4 KB | 表示 | |
CIF形式データ | 7tdt_validation.cif.gz | 83.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/td/7tdt ftp://data.pdbj.org/pub/pdb/validation_reports/td/7tdt | HTTPS FTP |
-関連構造データ
関連構造データ | 25838MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 255391.797 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ABCA1, ABC1, CERP / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O95477, P-type phospholipid transporter |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Human ABCA1 reconstituted into nanodiscs / タイプ: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / 由来: RECOMBINANT | ||||||||||||||||||||
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分子量 | 実験値: NO | ||||||||||||||||||||
由来(天然) | 生物種: Homo sapiens (ヒト) | ||||||||||||||||||||
由来(組換発現) | 生物種: Homo sapiens (ヒト) / 株: HEK | ||||||||||||||||||||
緩衝液 | pH: 8 | ||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.8 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES 詳細: Homogeneous, monodisperse sample of ABCA1 in nanodiscs | ||||||||||||||||||||
試料支持 | グリッドの材料: GOLD / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 | ||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company / モデル: Talos Arctica / 画像提供: FEI Company | |||||||||||||||||||||||||||
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EM imaging | アライメント法: COMA FREE / 電子線源: FIELD EMISSION GUN / 照射モード: FLOOD BEAM / モード: BRIGHT FIELD / Cs: 2.7 mm / Specimen-ID: 1
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撮影 |
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-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 364684 | ||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 32360 / アルゴリズム: BACK PROJECTION / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 5XJY PDB chain-ID: A | ||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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